Scandinavian brown bears that survived a severe population crash now carry more cavities in their teeth, and their dental plaque holds clues to why. Researchers will scrape calcified oral microbiome—dental calculus—from museum-preserved bear skulls to reconstruct how shrinking genetic diversity altered the bears’ mouth bacteria and disease patterns over time. The core problem is that host-associated microbiomes usually decay after death, making it nearly impossible to study how population declines affect host-microbe interactions in wild animals. Dental calculus preserves that microbial record. By combining ancient DNA techniques with metagenomics and population genomics, the team will create a new field they call Temporal Hologenomics—studying hosts and their microbiomes across centuries. If successful, the work will reveal whether loss of genetic diversity directly drives oral disease and pathogen evolution in wild populations. This is fundamental science with no immediate practical application, but the open-access analytical pipelines developed here could eventually be adapted for conservation biology—helping managers predict how endangered species’ health might shift as populations shrink—and for evolutionary or clinical studies of how host genetics shape microbial communities over long timescales.
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Symbiotic microbiomes play a central role in many biological processes and are intrinsically linked to host health. The composition of host-associated microbiomes is mediated by host genetics, which is particularly relevant to wild systems in the face of global climate change and rapid population declines. It is thus crucial to understand how changes in genetic diversity impact host-microbiome interactions. Achieving this goal in wild populations requires samples that span decades to centuries of population declines, yet host-associated microbiomes often do not preserve after host death. To address this significant knowledge gap, we will utilise dental calculus, the calcified oral microbiome, from museum-preserved specimens of Scandinavian brown bears that experienced a dramatic population bottleneck over the course of the last 200 years. Preliminary research in our group found an inverse relationship between the prevalence of dental caries (cavities resulting from tooth decay) and population size. The main research objectives of MetaBear are to investigate i) the role of host population genomics in the prevalence of oral disease, ii) how population declines and host genetics shape oral microbiomes, and iii) the evolution of oral pathogens and emergence of virulence factors. In a world first, we will integrate state-of-the-art ancient DNA techniques with metagenomics, population genomics and phylogenomics to establish a new field of research - Temporal Hologenomics, the study of hosts and microbiomes over time. Insights from MetaBear are intrinsically interdisciplinary and will have direct applications to conservation and evolutionary biology, as well as EU Green Deal and UN Sustainable Development Goals strategies. The open-access Temporal Hologenomic bioinformatic pipelines developed in this project will be taught in dedicated workshops, enhancing the uptake of this approach in evolutionary, clinical and conservation biology.
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